Yep.
When his LTSVP expires he has to leave. When he returns he will need to go through the whole exciting process of getting another LTSVP again.
(btw: AFAIK popping up to JB for a while is not considered good enough. I think like that come back you can't even get a 30 day visa. Must come back via the airport I think. But I could well be wrong on that so I'd advise you ask SIR about it. Also check if he needs to leave for a certain period of time before he returns.)
His applying for a PR without already holding an EP is not a very good idea as blokes who obtain PR based on marriage to a Singaporean - and not on the basis of being an EP holder (ie: technical & skilled programme) stand a rather good chance of getting to experience the joys of NS.
If PR is granted under first generation technical skilled migration then he is not liable for NS, but he will need to have a job to apply under that category.
Have you had a look at the SiR website yet? There is quite a bit of info there.
http://www.sir.gov.sg